| Variant ID: vg0222308618 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22308618 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGTGCTCTTAGTCATATCCATGAGTCAAAATATTTTTGGAATCATTTTTGAAAAATGATTTTCTCCCCGGGACAGAGAGGGCTACCCGGAGGTTCTGGC[C/T]
AGAACTTCCGGGTGCCGTTTAAAAGCAAAAATTTCCTAAGTGCTGCTTGGAAGTTCCTGGCACTTTTGCCCGGAACCTCCTGGCAGGTTTCCAGTTCAAA
TTTGAACTGGAAACCTGCCAGGAGGTTCCGGGCAAAAGTGCCAGGAACTTCCAAGCAGCACTTAGGAAATTTTTGCTTTTAAACGGCACCCGGAAGTTCT[G/A]
GCCAGAACCTCCGGGTAGCCCTCTCTGTCCCGGGGAGAAAATCATTTTTCAAAAATGATTCCAAAAATATTTTGACTCATGGATATGACTAAGAGCACTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.00% | 24.90% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 94.00% | 6.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 39.40% | 60.50% | 0.13% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.40% | 12.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 63.90% | 36.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 11.90% | 87.70% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 18.70% | 81.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 35.40% | 64.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 38.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222308618 | C -> T | LOC_Os02g36940.1 | downstream_gene_variant ; 3215.0bp to feature; MODIFIER | silent_mutation | Average:36.787; most accessible tissue: Minghui63 young leaf, score: 57.221 | N | N | N | N |
| vg0222308618 | C -> T | LOC_Os02g36924-LOC_Os02g36940 | intergenic_region ; MODIFIER | silent_mutation | Average:36.787; most accessible tissue: Minghui63 young leaf, score: 57.221 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222308618 | NA | 2.03E-07 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0222308618 | 3.80E-06 | NA | mr1124_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0222308618 | NA | 5.44E-07 | mr1908_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |